What is the best public database for Homo-sapiens proteins ?

Question

[ahmedmelmoselhy]

I have list of UniProt entries that corresponds to human proteins and I want the list domains composing those proteins. i.e I want the list of domains that exists in the first protein, then the second one, and so on. I found that there are many public databases that provide data about proteins (e.g. Pfam, Uniprot, InterPro, CATH). I am wondering what is the best one? Which one should I rely on while collecting this type of data?

[Jean-Karim Heriche]

Define best. Define domains. Each database has its own definition/way of identifying domains.

Answer 1

[Jean-Karim Heriche]

I prefer Ensembl. Because of the data integration in Ensembl, you just need to use only one database and one API throughout a project and annotations are then also consistent. Using multiple resources with different notions/definitions/APIs is a pain.

Answer 2

[keremwai]

Uniprot and Pfam are great and hand curated. I know less the others.

[ahmedmelmoselhy]

Thanks. For Pfam and UniProt, if I want to choose one of them, which is better ?

Answer 3

[Elisabeth Gasteiger]

You can upload your list of proteins using the batch retrieve service on the UniProt website (https://www.uniprot.org/uploadlists). Once you have your results, you can customize the layout of the table by adding or removing columns:

Click on "Columns" and then start typing "Pfam" (or "domain", for the UniProt domain annotations) into the search box that appears, and then select the relevant column name.

See also

• https://www.uniprot.org/help/customize

• (video, at about 1min25)

• Customise and share your search results: http://insideuniprot.blogspot.com/2015_03_01_archive.html

Answer 4

[Asaf]

Actually I really like GeneCards: https://www.genecards.org/